Locus 1642

Sequence ID 2L_DroMel_CAF1
Location 4,431,985 – 4,432,140
Length 155
Max. P 0.868846
window2633 window2634 window2635

overview

Window 3

Location 4,431,985 – 4,432,085
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 88.36
Mean single sequence MFE -23.54
Consensus MFE -19.79
Energy contribution -19.90
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.14
Structure conservation index 0.84
SVM decision value 0.53
SVM RNA-class probability 0.772823
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4431985 100 - 22407834
UGUUCGCCACCUCACCUUUCCACCAGCCCACCUGCUCACCUGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAAAUUGCUUCCUGUCCCAGUCUCCC
.........................(((((..(((((....)))))..)))))..(((((.(((.....(((.......)))....))))))))...... ( -26.60)
>DroSec_CAF1 37497 92 - 1
UG--------CUCACCUGUUCGCCACCUCACCUGCCCACCUGGGCAACUGGGCAUUUGGACACACACUCGCAUACAAAUUGCUUCCUGUCCCAGUCUCCC
..--------.....(((...(((....((..(((((....)))))..)))))....(((((.......(((.......)))....))))))))...... ( -21.30)
>DroSim_CAF1 41081 92 - 1
UG--------CUCACCUGUUCGCCACCUCUCCUGCCCACCGGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAAAUUGCUUCCUGUCCCAGUCUCCC
((--------((((...(((.(((.((.............)))))))))))))).(((((.(((.....(((.......)))....))))))))...... ( -22.72)
>consensus
UG________CUCACCUGUUCGCCACCUCACCUGCCCACCUGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAAAUUGCUUCCUGUCCCAGUCUCCC
................................(((((....)))))((((((((...(((......)))(((.......)))....)).))))))..... (-19.79 = -19.90 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,432,008 – 4,432,113
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 78.39
Mean single sequence MFE -23.07
Consensus MFE -8.59
Energy contribution -11.35
Covariance contribution 2.76
Combinations/Pair 1.25
Mean z-score -1.98
Structure conservation index 0.37
SVM decision value 0.18
SVM RNA-class probability 0.620516
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4432008 105 - 22407834
CAGGUGCUCACCAGUUCACCAGCUCACCUGUUCGCCACCUCACCUUUCCACCAGCCCACCUGCUCACCUGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAA
...(((((((.........(((.....))).......................(((((..(((((....)))))..)))))...))))))).............. ( -27.90)
>DroSec_CAF1 37520 97 - 1
CAGGUGCUCACCAAUUCACCAGUUCACCUG--------CUCACCUGUUCGCCACCUCACCUGCCCACCUGGGCAACUGGGCAUUUGGACACACACUCGCAUACAA
((((((..(............)..))))))--------......((((((....((((..(((((....)))))..))))....))))))............... ( -24.00)
>DroSim_CAF1 41104 97 - 1
CAGGUGCUCACCAGUUCACCAGUUCACCUG--------CUCACCUGUUCGCCACCUCUCCUGCCCACCGGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAA
...(((((((.(((.....(((.....)))--------.....)))...(((........(((((....)))))....)))...))))))).............. ( -25.20)
>DroEre_CAF1 39707 89 - 1
CAGGUGAGCACCAGUUCACCAGCGCACCAG--------CUCACCUGUUCGCCACCUCACCUUUCCACCUGCCCACC--------UGGGCACACACUCGCAUACAA
(((((((((....((......))......)--------))))))))......................(((((...--------.)))))............... ( -24.00)
>DroYak_CAF1 38465 89 - 1
CAGGUGCUCACCAGUUCACCAGCGCACCAGCUCACCAGCUCACCUGUUCGCCACCUCACCUUUCCA--------CC--------UGGGCACACACUCGCAUACAA
((((((......((((....(((......)))....))))))))))...(((..............--------..--------..)))................ ( -14.27)
>consensus
CAGGUGCUCACCAGUUCACCAGCUCACCUG________CUCACCUGUUCGCCACCUCACCUGCCCACCUGGGCAACUGGGCAUUUGGGCACACACUCGCAUACAA
((((((..................))))))..............((((((....(((...(((((....)))))...)))....))))))............... ( -8.59 = -11.35 +   2.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,432,048 – 4,432,140
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 71.96
Mean single sequence MFE -29.52
Consensus MFE -9.92
Energy contribution -10.98
Covariance contribution 1.06
Combinations/Pair 1.44
Mean z-score -2.24
Structure conservation index 0.34
SVM decision value 0.86
SVM RNA-class probability 0.868846
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4432048 92 + 22407834
GAGCAGGUGG-GCUGGUGGAAAGGUG-AGGUGGCGAA-CAGGUGAGCUGGUGAACUGGUGAGCACCUGGGGU-CAGCGAGCGGGCGUCAC---AAGAAU
......((((-(((.((.........-.(.((((...-((((((.((..(....)..))...))))))..))-)).)..)).))).))))---...... ( -31.60)
>DroSec_CAF1 37560 84 + 1
GGGCAGGUGA-GGUGGCGAACAGGUG-AG---------CAGGUGAACUGGUGAAUUGGUGAGCACCUGGGGU-CAGCGGGCGGGCGUCAC---AAGAAU
..........-.((((((..(.....-..---------((((((.((..(....)..))...))))))..((-(....))))..))))))---...... ( -25.70)
>DroSim_CAF1 41144 84 + 1
GGGCAGGAGA-GGUGGCGAACAGGUG-AG---------CAGGUGAACUGGUGAACUGGUGAGCACCUGGGGU-CAGCGGGCGGGCGUCAC---CAGAAU
..........-(((((((..(.....-..---------((((((.((..(....)..))...))))))..((-(....))))..))))))---)..... ( -33.00)
>DroEre_CAF1 39739 84 + 1
GGAAAGGUGA-GGUGGCGAACAGGUG-AG---------CUGGUGCGCUGGUGAACUGGUGCUCACCUGGGGU-CAGCGGGAGGGCGUCAC---AAAAAU
..........-.(((((((.((((((-((---------(......((..(....)..)))))))))))...)-).((......)))))))---...... ( -31.40)
>DroYak_CAF1 38489 92 + 1
GGAAAGGUGA-GGUGGCGAACAGGUG-AGCUGGUGAG-CUGGUGCGCUGGUGAACUGGUGAGCACCUGGGGU-CAGCGGGCAGGCGUCAC---AAAAAU
..........-.((((((..((((((-.((..((..(-(..(....)..))..))..))...))))))..((-(....)))...))))))---...... ( -34.50)
>DroPer_CAF1 48833 89 + 1
GGAAAGGUAUAUGUAUUGA-----UGUAUGUGGUAUGUAUGGUAUGUCUG-CAUCUGGUGGGC----GGAGUAAAGCGGGCAGGCAUUCCCCUAAAAAU
((((...((((((((((..-----.......))))))))))((.((((((-(.((((.....)----))).....))))))).)).))))......... ( -20.90)
>consensus
GGAAAGGUGA_GGUGGCGAACAGGUG_AG_________CAGGUGAGCUGGUGAACUGGUGAGCACCUGGGGU_CAGCGGGCGGGCGUCAC___AAAAAU
............(((((.......................((((.(((((....)))))...)))).........((......)))))))......... ( -9.92 = -10.98 +   1.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:25 2006